Remarkable Nucleotides

Mike Gene is devoting his time and energies to more important things these days but his blog entries are missed by many of you. Yet his book The Design Matrix and his many internet writings remain available. From time to time I'll reference a particular essay, blog or book discussion in a blog entry placed in a new category called Gene's Gems. The first references DNA-Binding: A Match Made in Heaven from The Design Matrix. Quoting:

Notice that it is more complex than an amino acid, where three complex chemical groups are covalently linked together. And unlike amino acids, nucleotides are not recovered in Miller-Urey type experiments. In fact, Robert Shapiro, professor emeritus of chemistry and senior research scientist at New York University, notes:

And no sample of a nucleotide, the building block of RNA or DNA, has ever been discovered in a natural source apart from Earth life. Or even take off the phosphate, one of the three parts, and no nucleoside has ever been put together. Nature has no inclination whatsoever to build nucleosides or nucleotides that we can detect, and the pharmaceutical industry has discovered this.

Another way of putting this is that nature rarely selects nucleotides, much less nucleic acids, as products of extracellular chemical reactions.

What is also remarkable about nucleotides is that it is possible to connect the sugar, phosphate group, and nitrogenous base together to form different structures.

In their book, The Mystery of Life’s Origins, Thaxton et al. calculate there are 45 different isomers of the above nucleotide. And when it comes to forming a dinucleotide, shown in the figure below, Thaxton et al. calculate 720 different ways of connecting things together.

So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function? Life found on earth is an outcome. It does not specify the sufficiency of a causal chain of primordial chemical reactions.

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171 Responses to “Remarkable Nucleotides”

Doug Says:
July 19th, 2008 at 2:02 pm
Bradford,
it's crazy you mentioned this because I was just chatting with a friend about Mike's article The Rational Essence of Proteins and DNA

Which includes A Match Made in Heaven.

It's a great read.

Comment by Doug — July 19, 2008 @ 2:02 pm

Doug Says:
July 19th, 2008 at 2:05 pm
Messed up the link…
but here it is:

The Rational Essence of Proteins and DNA

Comment by Doug — July 19, 2008 @ 2:05 pm

Thought Provoker Says:
July 19th, 2008 at 2:30 pm
Hi Bradford,

I am using my free weekend to catch up on the status of things like Orch OR and Nanobes.

Here is an abstract from interesting paper…

There have been several attempts to answer the question of whether there is, or has ever been, life on Mars. The boldest attempt was the only ever life detection experiment conducted on another planet: the Viking mission. The mission was a great success, but it failed to provide a clear answer to the question of life on Mars. More than 30 years after the Viking mission our understanding of the history and evolution of Mars has increased vastly to reveal a wetter Martian past and the occurrence of diverse environments that could have supported microbial life similar to that on Earth for extended periods of time. The discovery of Terran extremophilic microorganisms, adapted to environments previously though to be prohibitive for life, has greatly expanded the limits of habitability in our Solar System, and has opened new avenues for the search of life on Mars. Remnants of a possible early biosphere may be found in the Martian meteorite ALH84001. This claim is based on a collection of facts and observations consistent with biogenic origins, but individual links in the collective chain of evidence remain controversial. Recent evidence for contemporary liquid water on Mars and the detection of methane in the Martian atmosphere further enhance the case for life on Mars. We argue that, given the cumulative evidence provided, life has and is likely to exist on Mars, and we have already found evidence of it. However, to obtain a compelling certainty a new mission is needed, one which is devoted to the detection of life on Mars.

As you may recall, the meteorite ALH84001 had Nanobes similar to those recently discovered in sandstones and, possibly, our blood system.

The curious thing about Nanobes is that they appear to contain nucleotides and grow in colonies. However, it is still argued whether or not Nanobes are life.

Considering the shortening time frame due to the determination that the orgin of life predates an RNA World it is becoming less and less likely that OOL occured on "primordial earth".

While you may perfer your presumed hypothesis that life poofed into existance on Earth, the trail of scientific evidence may be leading to a Third Choice.

Shall we follow the evidence wherever it leads?

Then the Lord answered Job from the whirlwind: "Why are you using your ignorance to deny my providence?"- Job38:1-2

Comment by Thought Provoker — July 19, 2008 @ 2:30 pm

Bradford Says:
July 19th, 2008 at 2:40 pm
TP, someone at TT once pointed to a paper indicating that material exchanges between Mars and the earth, over eons of time, have involved considerable tonnage. I do not understand the mechanics of this but if true it would complicate an effort to ascertain what originated where.

I don't contend that life resulted from magic. That's critic spin. Purposeful input is a more accurate portrayal.

Comment by Bradford — July 19, 2008 @ 2:40 pm

Raevmo Says:
July 19th, 2008 at 3:11 pm
Bradford:

So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

Here's an answer to that question:

But for Morowitz, the most exciting development in the metabolism-first camp, “the really new idea,” is that small organic molecules, such as amino acids, can catalyze the formation of other small organic molecules, such as nucleic acids. “This has emerged only in the last two years,” he says. This view has found strong support from a new finding published in the journal Chemistry in August 2005, which indicates that single amino acids can catalyze the creation of sugars from simple starting materials with enzyme-like specificity.

“What has emerged is a very strong self-organizing principle,” says Morowitz. In this view, while iron sulfide may have been the original catalyst, it did not remain the only one for long. As products of the original reactions catalyzed new reactions, metabolic networks quickly arose. Feedback loops developed when two molecules regulated one another's synthesis. “The system can piggyback its way upward,” he says.

While the study of such networks is still in its infancy, Morowitz suggests they hold the key to a host of knotty problems, including that of RNA synthesis. “It's not a problem in this network point of view. Very early on you get the precursor compounds,” while formation of the complete nucleotide arises later. “Even today this is the core network of biochemistry.”

From http://biology.plosjournals.or...

What do you think, Bradford?

Comment by Raevmo — July 19, 2008 @ 3:11 pm

Thought Provoker Says:
July 19th, 2008 at 4:20 pm
Hi Bradford,

Since this thread appears to a kind of tribute to Mike Gene, I thought you would appreciate me posting a topical exchange he and I had a while back (last August).

First, my comment….

Hi Mike,

You wrote…

The bias is a function of pragmatism… This brings me to ID101.

Of course, just because it is a presumption that is built on experience doesn't mean it is not a presumption. Thus yes, I am quite open to other alternatives. But the key here again is pragmatism. I have to find it useful.

My immediate reaction was an urge to question how much of the pragmatism and usefulness is due to the ready-made group think and supporting movement. However, saying something would be rude, crude and socially unacceptable(that and I don't want you to change your mind about guest hosting my other post). Therefore, I will entertain the mind set you are suggesting.

Engaging open mindedness mode in 5… 4… 3…

A long time ago, Larry Niven wrote a science fiction story, World of Ptavs. Mr. Niven was adept at investigating intriguing questions through his stories. This story is particularly relevant since not only does it deal with the concept of human-like intelligence being responsible for the origin of life on Earth, it provided an explanation for the paradoxical nature of life's design, why there is no "signature" buried in the design and why SETI hasn't found any evidence of alien intelligence.

[ponders leaving this as a cliff hanger... "nah, I'll be nice"]

Once upon a time there was an intelligent alien race called "Thrints". The Thrints' mental abilities were such that they could control other conscious beings. This came in handy since Thrints were also voracious carnivores. They could just will food to come to them.

There was another advanced alien race called "Tnuctipun". Unfortunatly for the Tnuctipun, they happened upon the Thints during their space explorations. Tnuctipun had stasis fields, spaceships, genetic biologics and all manner of advanced knowledge. However, the Tnuctipun mind was especially susceptible to being controlled by the Thrints. The Thrints were an arrogant race. They judged worth based on what made them special, their mental abilities. Everything else was food which they referred to as ptavs.

When they arrived, the Thrints were able to restrain themselves long enough to be convinced the Tnuctipun had a potential beyond being entrÃ©es. The Thrints ordered the Tnuctipun to design and setup sources of food on other planets throughout the galaxy. The only living thing a Thrint feared was another Thrint. Therefore, these food planets were purposely set up to have large interstellar distances between them. Since there is no such thing as faster-than-light travel this provided effective protection allowing a Thrint and his family to live and eat in peace. Earth is one of these food planets, a "World of Ptavs".

So what happened?

Earth's owner, Kzanol, had a mishap on his way to his new home. Without Kzanol's maintenance (a single Thrint with an amplifier helmet can easily control and entire planet of ptavs) Earth's development was mostly unorganized and "wild". Think of a long-abandoned garden.

——————————————————

While I have deviated slightly from Niven's story line that isn't important (I would be impressed if someone could point out my deviations). In Niven's story Kzanol crash landed on Earth billions of years ago protected by his stasis field (where time stands still). The "intelligent" ptavs on Earth release Kzanol from stasis which sets up the plot-line of where Kzanol tries to get to his amplifier helmet (dropped off on Uranus) before the telepathic hero trying to save Earth. There is also the twist that Kzanol is the last living Thrint because the Thrints were wiped out (along with the Tnuctipun) after the Tnuctipun were ordered to design and create large brained cows called Bandersnatch with immunity to mind control so the Thrint could hunt them for sport. For all their mental powers, it turned out the Thrint weren't very bright.

But back to the allegedly non-fictional discussion concerning the concepts of Intelligent Design. While Niven's story would probably be considered designer centric, it potentially illustrates unwarranted presumptions. What possible reason do we have for presuming a single designer intended for life on Earth to evolve as it has?

Mike, you allow for the possibility of multiple designers but why do you allow for the possibility of a single designer? We can play the anything-is-possible game of probabilities, but hopefully we can get beyond that. If someone like Aagcobb said he estimates the probability of a single designer intentionally creating life on Earth to be "at close to zero" would you find that reasonable or "effectively black-and-white thinking"? My response to Aagcobb would be to ask about the probabilities that Earth was accidentally seeded by a meteorite in an attempt to explore his gray areas.

IMO. a suggestion that a single, unidentified intelligent being intentionally created life on Earth as more likely than an errant meteorite approaches wistful fiction considering we have evidence for the latter and practically none for the former(note: God is an identified designer).

If there are intelligent aliens running around, why wouldn't it be likely Earth's seeding was accidental? An interstellar passenger liner just happened to purge it's biological waste tank in this general vicinity billions of years ago. You know the chuck a material we found in Antarctica we THOUGHT was a meteorite? Well….

Some people might not find the idea of life on Earth being the result of contamination an intriguing idea, but I do regardless of whether it happened via a meteorite or some other … err um … material.

The point of this long-winded comment is an attempt to illuminate the general bias I have noticed in the presumption that human-like mental abilities are considered indispensable to the point of not only ascribing the them to designer(s) but also presuming it is a goal of the design.

It's the kind of the presumption a Thrint would make.

link

Here was Mike Gene's response…

Hi TP,

Liked the synopsis.

IMO. a suggestion that a single, unidentified intelligent being intentionally created life on Earth as more likely than an errant meteorite approaches wistful fiction considering we have evidence for the latter and practically none for the former(note: God is an identified designer).

Of course it approaches fiction (although the adjective wistful does not apply). The acknowledgement of no independent evidence for unidentified intelligent beings intentionally created life on Earth is the starting place for my inquiries.

If there are intelligent aliens running around, why wouldn't it be likely Earth's seeding was accidental? An interstellar passenger liner just happened to purge it's biological waste tank in this general vicinity billions of years ago. You know the chuck a material we found in Antarctica we THOUGHT was a meteorite? Well…".

Indeed! In fact, somewhere in the 1000s of postings I have made over the years, I think I raised this very issue.

Some people might not find the idea of life on Earth being the result of contamination an intriguing idea, but I do regardless of whether it happened via a meteorite or some other… err um… material.

I agree it's intriguing. So too is the notion that this is all an experiment.

The point of this long-winded comment is an attempt to illuminate the general bias I have noticed in the presumption that human-like mental abilities are considered indispensable to the point of not only ascribing the them to designer(s) but also presuming it is a goal of the design.

I ascribe human-like mental abilities to the designer(s) because I have experience with human-like mental abilities. However, you err if you think that I envision human-like mental abilities as an indispensable goal of the design. That position is embedded in Aagcobb's attempt to falsify ID, not my approach.

Comment by MikeGene — August 11, 2007 @ 9:52 am

link

This is not about suggesting "magic". It doesn't require magic for an identified designer (God) to provide "purposeful input" into creating life on Earth while he/she/it was creating the universe. That point is moot and is meaningless in the exploration of the natural mechanisms by which such a God's design unfolded.

God or no God, those of us interesting in exploring explanations and following the evidence wherever it leads are interested in assessing the plausibilities of these explanations.

It does not seem plausible that a single, unidentified designer intentionally seeded the earth four billion years ago (six thousand maybe but not four billion).

There is no scientific evidence supporting that contention and defies sensibilities unless one presumes a meddlesome deity.

If life on Earth was intentionally seeded four billion years ago then, at the very least, one should presume multiple and probably conflicting designers.

However, once you accept the possibility of intelligent beings running around you need to take accidental contamination into consideration.

Contamination doesn't need to be direct. It could also be something inherent in space (Nanobes floating in space?).

It is something to think about. Mike Gene did and, presumably, still does.

Comment by Thought Provoker — July 19, 2008 @ 4:20 pm

Zachriel Says:
July 19th, 2008 at 10:44 pm
Bradford: So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

Unrau and Bartel, RNA-catalyzed nucleotide synthesis, Nature.

The citations are worth a read.

Oró, Mechanism of synthesis of adenine from hdyrogen cyanide under possible primitive earth conditions, Nature.

Sanchez, Ferris and Orgel, Studies in prebiotic synthesis, Synthesis of purine precursors and amino acids from aqueous hydrogen cyanide, J. Mol. Biol.

Ferris, Sanchez and Orgel, Studies in prebiotic synthesis. 3. Synthesis of pyrimidines from cyanoacetylene and cyanate, J. Mol. Biol.

Stoks and Schwartz, Uracil in carbonaceous meteorites, Nature

Robertson and Miller, An efficient prebiotic synthesis of cytosine and uracil, Nature.

This is rather old stuff. Here's something a bit more recent.

Yuasa, Flory, Basile and Oró, Abiotic synthesis of purines and other heterocyclic compounds by the action of electrical discharges, J. Mol. Biol.

Comment by Zachriel — July 19, 2008 @ 10:44 pm

Thought Provoker Says:
July 19th, 2008 at 11:59 pm
Hi Zachriel,

Thank you for your post. I found the citation about carbonaceous meteorites interesting enough to go looking and found this recent paper titled…

Extraterrestrial nucleobases in the Murchison meteorite

Here is the abstract…

"Carbon-rich meteorites, carbonaceous chondrites, contain many biologically relevant organic molecules and delivered prebiotic material to the young Earth. We present compound-specific carbon isotope data indicating that measured purine and pyrimidine compounds are indigenous components of the Murchison meteorite. Carbon isotope ratios for uracil and xanthine of δ13C=+44.5‰ and +37.7‰, respectively, indicate a non-terrestrial origin for these compounds. These new results demonstrate that organic compounds, which are components of the genetic code in modern biochemistry, were already present in the early solar system and may have played a key role in life's origin."

Since this is a 2008 paper written by scientists from…

a Astrobiology Laboratory, Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands

b Department of Earth Science and Engineering, Imperial College, London, SW7 2AZ, UK

c NASA Goddard Space Flight Center, Code 699, Greenbelt, MD 20771, USA

d Goddard Earth Sciences and Technology Center, University of Maryland Baltimore, County, Baltimore, MD 21228, USA

e GL, Carnegie Institution of Washington, Washington, DC 20015, USA

f Planetary and Space Sciences Research Institute, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK

g Radboud University Nijmegen, 6525 ED, Nijmegen,The Netherlands

…it looks like the extraterrestrial contamination explanation for OOL might be taking hold in scientific circles.

Comment by Thought Provoker — July 19, 2008 @ 11:59 pm

Zachriel Says:
July 20th, 2008 at 8:43 am
Thought Provoker: …it looks like the extraterrestrial contamination explanation for OOL might be taking hold in scientific circles.

The distinction between terrestrial and extraterrestrial was not so distinct in those days, and material was continually being exchanged. The Earth's surface water may also have a cometary origin.

Comment by Zachriel — July 20, 2008 @ 8:43 am

Bradford Says:
July 20th, 2008 at 1:16 pm
So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

Raevmo: Here's an answer to that question:

But for Morowitz, the most exciting development in the metabolism-first camp, “the really new idea,” is that small organic molecules, such as amino acids, can catalyze the formation of other small organic molecules, such as nucleic acids. “This has emerged only in the last two years,” he says.

The startling thing about the statement is the comment that:

“the really new idea,” is that small organic molecules, such as amino acids, can catalyze the formation of other small organic molecules, such as nucleic acids.

A basic familiarity with cellular function would have revealed that amino acids have catalytic properties. Most enzymes, after all, are amino acid polymers. A few specified amino acids binding nucleic acid bases or ribose sugars can be part of a catalytic reaction. The more interesting matter is a detailed description of what extra-cellular conditions give rise to amino acids, nitrogenous bases, ribose sugars and phosphate groups and what circumstances allow for a reasonable degree of homeostasis that would not only make the anticipated reactions possible, but would also protect against mitigating side reactions.

My main objection to current ideas is not that extracellular reactions, giving rise to biomolecules, will not happenn. Rather that none of this addreeses a core problem OOL must face i.e. accounting for specified sequencing of polymers needed for biological function. That however will be the subject of a separate blog entry.

Comment by Bradford — July 20, 2008 @ 1:16 pm

Zachriel Says:
July 21st, 2008 at 8:48 am
Bradford: So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

So we have the natural synthesis of macromolecules, such as purines and amino acids. We have RNA-catalysed nucleotide synthesis. We have random nucleotide sequences capable of autocatalysis and evolution. Segregation via lipid membranes and competing metabolic networks seem plausible. There's no complete theory, but there doesn't appear to be any inherent barrier and a lot of supporting evidence.

Comment by Zachriel — July 21, 2008 @ 8:48 am

Bradford Says:
July 21st, 2008 at 11:31 am
Zachriel: There's no complete theory, but there doesn't appear to be any inherent barrier and a lot of supporting evidence.

No inherent barrier as in the laws of nature do not make it impossible? That would be a weak thread on which to hang a theory. There is much supporting evidence for the fact that biomolecules chemically react with one another.

Comment by Bradford — July 21, 2008 @ 11:31 am

Zachriel Says:
July 21st, 2008 at 11:37 am
Bradford, you asked this question.

Bradford: So the question is: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

You have been provided a variety of evidence.

Comment by Zachriel — July 21, 2008 @ 11:37 am

Bradford Says:
July 21st, 2008 at 11:44 am
You have been provided a variety of evidence.

I was looking for non-trivial evidence. I already knew that nucleotide and amino acid polymers can have catalytic effects. An extracellular process, with a cell in mind as the end result, needs to point to something much more substantial.

Comment by Bradford — July 21, 2008 @ 11:44 am

Zachriel Says:
July 21st, 2008 at 12:54 pm
Bradford: I was looking for non-trivial evidence.

It is hardly trivial. The discovery of the catalytic properties of RNA won a Nobel Prize, and it is certainly pertinent evidence.

Bradford: An extracellular process, with a cell in mind as the end result, needs to point to something much more substantial.

No one claimed to have a complete theory of abiogenesis.

Comment by Zachriel — July 21, 2008 @ 12:54 pm

Bradford Says:
July 21st, 2008 at 1:02 pm
Bradford: I was looking for non-trivial evidence.

Zachriel: It is hardly trivial. The discovery of the catalytic properties of RNA won a Nobel Prize, and it is certainly pertinent evidence.

And that's old news.

Comment by Bradford — July 21, 2008 @ 1:02 pm

Zachriel Says:
July 21st, 2008 at 1:13 pm
Bradford: And that's old news.

Yes, and the Earth still moves. You've been provided evidence, old and new. The evidence doesn't disappear just because you wave your hands.

Comment by Zachriel — July 21, 2008 @ 1:13 pm

Bradford Says:
July 21st, 2008 at 1:37 pm
Zachriel:

Yes, and the Earth still moves. You've been provided evidence, old and new. The evidence doesn't disappear just because you wave your hands.

I've been provided with evidence that some biomolecules have catalytic functions and autocatalytic properties. Old news. What I've asked for and gotten hand waving responses to is what is the basis for assuming the end result of a cell from an SRM starting point? That question will not disappear with song and dance responses.

Comment by Bradford — July 21, 2008 @ 1:37 pm

Zachriel Says:
July 21st, 2008 at 2:04 pm
This was your question:

Bradford: what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?

* All living functions have a chemical basis.
* All organisms evolved from primitive ancestors.
* Organic macromolecules spontaneously assemble in primodial conditions, including the fundamental building blocks of replication and enzymatic activity.
* RNA can catalyze nucleotide synthesis.
* Random sequences can result in enzymatic activity, including autocatalysis.
* Evolution is inherent in imperfect replicators replicating imperfectly.
* There are plausible mechanisms for the origin of segregating membranes and of metabolism.
* There are no known inherent barriers to abiogenesis.

This evidence forms a basis for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function.

Comment by Zachriel — July 21, 2008 @ 2:04 pm

Bradford Says:
July 21st, 2008 at 2:10 pm
Zachriel:

Evolution is inherent in imperfect replicators replicating imperfectly.

Is this a new law of chemistry? Or does evolution also encompass the degradation of an RNA molecule? The theme of my questions is direction. Where's the directional indicator indicating molecular evolution towards a cell?

Comment by Bradford — July 21, 2008 @ 2:10 pm

chunkdz Says:
July 21st, 2008 at 2:28 pm
Z,

* There are no known inherent barriers to abiogenesis.

Racemization?

Comment by chunkdz — July 21, 2008 @ 2:28 pm

chunkdz Says:
July 21st, 2008 at 2:41 pm
* There are no known inherent barriers to abiogenesis.

cytosine deamination?

Comment by chunkdz — July 21, 2008 @ 2:41 pm

chunkdz Says:
July 21st, 2008 at 2:42 pm
* There are no known inherent barriers to abiogenesis.

hydrolysis?

Comment by chunkdz — July 21, 2008 @ 2:42 pm

Zachriel Says:
July 21st, 2008 at 3:41 pm
Bradford: The theme of my questions is direction. Where's the directional indicator indicating molecular evolution towards a cell?

That wasn't in your original question, which I have answered.

Evolutionary processes have no particular direction, but as I already pointed out, there are plausible mechanisms of segregation which would provide competitive benefits. Remember that there is no complete theory of abiogenesis, so it seems you are just ignoring what is known.

chunkdz: Racemization? Cytosine deamination? Hydrolysis?

Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process. I have no idea what you think cytosine deamination has to do with this. Hydrolysis may have a solution in segregating membranes. But regardless, these are not *inherent* barriers (meaning one without any possible resolution).

Comment by Zachriel — July 21, 2008 @ 3:41 pm

Bradford Says:
July 21st, 2008 at 4:00 pm
Zachriel: Evolutionary processes have no particular direction,

You can make that claim when looking from the perspective of a starting point. But in retrospect we can observe the end products of a causal chain which included cells. So whether evolution had a direction the causal chain of actual events very definitely had one- a specifiable, observable outcome. Incidentally, front loading is directionally oriented as distinguished from a process you have in mind.

but as I already pointed out, there are plausible mechanisms of segregation which would provide competitive benefits.

What constitues a competitive benefit to a molecule? A self-catalytic reaction is still a chemical reaction as opposed to biological systems involving many interacting parts with identifiable functions.

Remember that there is no complete theory of abiogenesis, so it seems you are just ignoring what is known.

I'm not ignoring what is known. In fact I'm highlighting some other known physical phenomenon that would not bode well for abiogenesis. I don't want a politicized analysis where only data favorable to a particular paradigm is touted.

Comment by Bradford — July 21, 2008 @ 4:00 pm

chunkdz Says:
July 21st, 2008 at 4:02 pm
Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

Ho hum. Another appeal to luck.

Hydrolysis may have a solution in segregating membranes.

*Yawn* Now it's lucky bubbles.

Zachriel, what *WOULD* you consider to be an inherent barrier to your unknown, unseeable mystery process?

Comment by chunkdz — July 21, 2008 @ 4:02 pm

Zachriel Says:
July 21st, 2008 at 4:44 pm
Bradford: But in retrospect we can observe the end products of a causal chain which included cells. So whether evolution had a direction the causal chain of actual events very definitely had one- a specifiable, observable outcome.

Yes, and there is a strongly supported Theory of Evolution which explains that pattern in living organisms. We see the end result, but not the extensive branching that led nowhere, so the pattern has the resemblance of direction. In fact, we can directly observe this pattern. It's almost as if the bacteria intend to evolve in response to the particular antibiotic found in their environment, but we can show that the process is random with respect to fitness.

Bradford: What constitues a competitive benefit to a molecule?

One that makes more of the same molecule (or interacting network).

Bradford: In fact I'm highlighting some other known physical phenomenon that would not bode well for abiogenesis.

nucleotides are not recovered in Miller-Urey type experiments

This is rather old stuff.

Comment by Zachriel — July 21, 2008 @ 4:44 pm

Zachriel Says:
July 21st, 2008 at 4:45 pm
Zachriel: Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

chunkdz: Ho hum. Another appeal to luck.

It's not luck to say that a coin will land either heads or tails. Do you understand the Law of Small Numbers and how it applies to fixation?

There aren't enough small numbers to meet the many demands made of them. — Richard Guy

chunkdz: what *WOULD* you consider to be an inherent barrier to your unknown, unseeable mystery process?

I am pointing to strong evidence of a link between chemistry and life. Every observation thus far supports the view that life arose from natural processes. There is no evidence of teleology in the origin of life.

Many ID Advocates point to plausible problems with this or that theory of abiogenesis thinking that pointing to a Gap means it is an insurmountable gap (an inherent barrier), as you just did. It would behoove ID Advocates to actually propose and test scientific hypotheses.

Comment by Zachriel — July 21, 2008 @ 4:45 pm

Bradford Says:
July 21st, 2008 at 5:00 pm
Bradford: What constitues a competitive benefit to a molecule?

Zachriel: One that makes more of the same molecule (or interacting network).

Why the telic attachment of competition to molecules? Why even depict chemical reactions in this manner? Biomolecules are no different than other types in that bonding between molecules is predictable based on factors like the identity, proximity and number of different types of molecules present as well as energy requirements. Why assume that a series of reactions, vaguely described, led to a cell? If the amount of reaction products is the benefit indicator, then OOL is in worse shape than I thought. By merely starting with different chemicals one could use a selection scenario to favor any desired outcome. It is not nature driving this theory.

Comment by Bradford — July 21, 2008 @ 5:00 pm

chunkdz Says:
July 21st, 2008 at 5:03 pm
Zachriel,

Many ID Advocates point to plausible problems with this or that theory of abiogenesis thinking that pointing to a Gap means it is an insurmountable gap (an inherent barrier), as you just did.

So what would be an example of an inherent barrier?

Comment by chunkdz — July 21, 2008 @ 5:03 pm

Bradford Says:
July 21st, 2008 at 5:14 pm
Zachriel:

Many ID Advocates point to plausible problems with this or that theory of abiogenesis thinking that pointing to a Gap means it is an insurmountable gap (an inherent barrier), as you just did.

Plausible problems are not gaps in knowledge. Problems, highlighted with respect to standard approaches, may suggest a flawed approach that is a barrier to our perception of what drove an event. Constraint is a more useful term than barrier. By not recognizing constraints in a theorized physical process, reality is ignored.

Comment by Bradford — July 21, 2008 @ 5:14 pm

Doug Says:
July 21st, 2008 at 5:21 pm
Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

Hi Zach,
Maybe not an inherent barrier, but the plausibility drops.
Even in the absense of racemic nucleotides, the formation of one d-nucleotide has 45 different isomers. A dinucleotide there are 720 isomers (The Mystery of Life's Origin & Mike's linked paper). Incorporate both enantiomers and the likelihood gets even more muddy.

Comment by Doug — July 21, 2008 @ 5:21 pm

chunkdz Says:
July 21st, 2008 at 5:29 pm
Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

The salient point being that there is no such thing as an inherent barrier to an imaginary process.

There's no inherent barrier to building a space colony on the sun. It's just that the air conditioner would have to be very reliable. Just a gap in current knowledge, right Zach?

Comment by chunkdz — July 21, 2008 @ 5:29 pm

Raevmo Says:
July 21st, 2008 at 6:59 pm
Morowitz in the paper I cited:

“the really new idea,” is that small organic molecules, such as amino acids, can catalyze the formation of other small organic molecules, such as nucleic acids.

According to Bradford this is a "startling comment" because:

A basic familiarity with cellular function would have revealed that amino acids have catalytic properties. Most enzymes, after all, are amino acid polymers.

The arrogance of ignorance raises its ugly head once again. As if the expert Morowitz doesn't have such basic familiarity, but Bradford does. Unlike Bradford, Morowitz knows that a polymer having catalytic properties doesn't imply that the monomers have this property too.

Now we have seen some evidence that nucleotides are not as unlikely to form extracellularly as Bradford's OP suggests. Do you agree, Bradford? If so, does this increase the plausibility of abiogenesis?

Comment by Raevmo — July 21, 2008 @ 6:59 pm

Todd Berkebile Says:
July 21st, 2008 at 7:53 pm
Bradford: No inherent barrier as in the laws of nature do not make it impossible? That would be a weak thread on which to hang a theory.

This from the guy who prefers theories about a designer who can craft the laws of nature by his will.

Bradford: I was looking for non-trivial evidence. I already knew that nucleotide and amino acid polymers can have catalytic effects. An extracellular process, with a cell in mind as the end result, needs to point to something much more substantial.

So if I demand evidence that your designer actually exists I am being unreasonable, yet you can demand what, an ordered list of the millions of individual chemical reactions that lead from abiotic to biotic? Your standards of evidence seem heavily tilted by your biases (of course you will likely simply chant something about rubber and glue).

Bradford: Why the telic attachment of competition to molecules?

I need a name for the common practice of trying to thrust your attributes onto your opponent. "Telic attachment" doesn't even make sense, yet you obviously wanted to throw that term at Zachriel. At best you are projecting your inherent biases onto Zachriel, as nothing he said implied anything telic by my reading.

Bradford: Why assume that a series of reactions, vaguely described, led to a cell?

Because there is much evidence to support this notion. Why assume that a series of reactions could not possibly lead to a cell?

Comment by Todd Berkebile — July 21, 2008 @ 7:53 pm

Bradford Says:
July 21st, 2008 at 8:02 pm
Bradford: I was looking for non-trivial evidence. I already knew that nucleotide and amino acid polymers can have catalytic effects. An extracellular process, with a cell in mind as the end result, needs to point to something much more substantial.

Todd: So if I demand evidence that your designer actually exists I am being unreasonable, yet you can demand what, an ordered list of the millions of individual chemical reactions that lead from abiotic to biotic? Your standards of evidence seem heavily tilted by your biases (of course you will likely simply chant something about rubber and glue).

I have not demanded evidence for an entire process. At this point I have repeatedly asked for and received no responses to the question of why changes in an SRM would be selected which favor the development of a cell. If this is a scientific endeavor my question needs to be answered because it is basic to your theory.

Bradford: Why the telic attachment of competition to molecules?

I need a name for the common practice of trying to thrust your attributes onto your opponent. "Telic attachment" doesn't even make sense, yet you obviously wanted to throw that term at Zachriel. At best you are projecting your inherent biases onto Zachriel, as nothing he said implied anything telic by my reading.

Zachriel was the one who claimed that molecules compete with one another. That sounds telic to me and unlike the chemistry I learned from those who knew it well.

Bradford: Why assume that a series of reactions, vaguely described, led to a cell?

Because there is much evidence to support this notion.

There is not. There are SRMs that replicate to become SRMs for a limited period of time.

Why assume that a series of reactions could not possibly lead to a cell?

Science is about confirming evidence. We don't need to assume anything if it is there.

Comment by Bradford — July 21, 2008 @ 8:02 pm

Bradford Says:
July 21st, 2008 at 8:06 pm
Unlike Bradford, Morowitz knows that a polymer having catalytic properties doesn't imply that the monomers have this property too.

Now we have seen some evidence that nucleotides are not as unlikely to form extracellularly as Bradford's OP suggests. Do you agree, Bradford? If so, does this increase the plausibility of abiogenesis?

You have monomers and polymers with catalytic properties. Now answer the question others have avoided. In an extracellular environment why would selection act to preserve products that are essential components of cells?

Comment by Bradford — July 21, 2008 @ 8:06 pm

Todd Berkebile Says:
July 21st, 2008 at 8:43 pm
Bradford: I have not demanded evidence for an entire process. At this point I have repeatedly asked for and received no responses to the question of why changes in an SRM would be selected which favor the development of a cell.

This question assumes that the cell was a desired outcome. We have no reason to think "cell exactly as cells are today" was the selected feature. All we can reason is that whatever the selected attribute was the cell contained more of that attribute than whatever it was competing against.

Bradford: Zachriel was the one who claimed that molecules compete with one another. That sounds telic to me and unlike the chemistry I learned from those who knew it well.

I know that it sounds telic to you, everything sounds telic to you. I am suggesting this represents a fundamental difference in your thought processes compared to, say, me for whom it doesn't have any telic implications at all.

Todd: Because there is much evidence to support this notion.
Bradford: There is not. There are SRMs that replicate to become SRMs for a limited period of time.

Well you must just be smarter than all those scientists who won Nobel Prizes discovering all that evidence.

Bradford: Science is about confirming evidence. We don't need to assume anything if it is there.

And yet to make progress we must choose some hypothesis to test. So we assume the hypothesis with the most evidence supporting it and try to prove it wrong. When we fail to prove it wrong then it gains acceptance. ID has yet to generate a single hypothesis so they haven't even entered the game yet.

Comment by Todd Berkebile — July 21, 2008 @ 8:43 pm

Todd Berkebile Says:
July 21st, 2008 at 8:45 pm
Bradford: In an extracellular environment why would selection act to preserve products that are essential components of cells?

Because those components are also essential components (or perhaps waste products) of an extracellular replication process?

Comment by Todd Berkebile — July 21, 2008 @ 8:45 pm

Bradford Says:
July 21st, 2008 at 8:54 pm
Because those components are also essential components (or perhaps waste products) of an extracellular replication process?

Todd, have a beer and watch a ballgame.

Comment by Bradford — July 21, 2008 @ 8:54 pm

Zachriel Says:
July 21st, 2008 at 9:22 pm
Bradford: Why the telic attachment of competition to molecules?

Telic attachment? Huh?

In any case, we can observe the process of evolution among sequences of RNA. Check out Bartel's RNA Theme Park.

Bradford: Why assume that a series of reactions, vaguely described, led to a cell?

Who merely assumes such a thing? We hypothesize, then test for the entailed empirical predictions. Then we modify or discard our hypothesis.

Bradford: Zachriel was the one who claimed that molecules compete with one another. That sounds telic to me and unlike the chemistry I learned from those who knew it well.

In vitro molecular evolution dates from the early 1990's with the evolution of ribozyme ligases by Bartel and Szostak.

Bradford: In an extracellular environment why would selection act to preserve products that are essential components of cells?

What we would expect is that adaptive characteristics would be selected for current function.

Here's an interesting experiment that explores the threshold.

The Emergence of Competition Between Model Protocells, Chen, Roberts and Szostak, Science:

The transition from independent molecular entities to cellular structures with integrated behaviors was a crucial aspect of the origin of life. We show that simple physical principles can mediate a coordinated interaction between genome and compartment boundary, independent of any genomic functions beyond self-replication. RNA, encapsulated in fatty acid vesicles, exerts an osmotic pressure on the vesicle membrane that drives the uptake of additional membrane components, leading to membrane growth at the expense of relaxed vesicles, which shrink. Thus, more efficient RNA replication could cause faster cell growth, leading to the emergence of Darwinian evolution at the cellular level.

Comment by Zachriel — July 21, 2008 @ 9:22 pm

JOHN_A_DESIGNER Says:
July 21st, 2008 at 11:14 pm
Many of you were shocked when our leader, Mike Gene, decided to leave Telic Thoughts. Well tonight I have more shocking news. I have decided to switch sides. Well, okay I’m just going to pretend that I’m switching. Why? I have always been driven by a curiosity why people think the way they do. In other words, I really want understand the thought process you guys use in forming your arguments; and what better way is there than try to assume your point of view.

You can choose to help me if you wish. I will be honestly trying to represent your point of view. Of course if you don’t, then don’t. But it would seem to me that it would be in your interest to help me represent your arguments as accurately as possible. Remember that famous line from the movie, “Jerry McQuire:” “Help me, help you… Help me, help you…” Besides it might be fun.

Let me start with this:

Bradford asked, “what basis do we have for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function?”

Zachriel responded with:
* All living functions have a chemical basis.
* All organisms evolved from primitive ancestors.
* Organic macromolecules spontaneously assemble in primodial conditions, including the fundamental building blocks of replication and enzymatic activity.
* RNA can catalyze nucleotide synthesis.
* Random sequences can result in enzymatic activity, including autocatalysis.
* Evolution is inherent in imperfect replicators replicating imperfectly.
* There are plausible mechanisms for the origin of segregating membranes and of metabolism.
* There are no known inherent barriers to abiogenesis.
This evidence forms a basis for believing that primordial earth had conditions favorable to generating nucleotides in configurations that would be favorable to cellular function.

I think what Zachriel is trying to say here, Bradford, is that if we extrapolate the evolutionary process, which we already know is a completely natural process, backwards in time we find that there are simple organisms that evolve from simpler organism’s and we keep getting simpler and simpler and simpler till we reach a point where we have only organic compounds.

Experiments like Stanley Millers abiogenesis experiment have demonstrated that given the right conditions certain organic molecules like amino acids can be formed rather easily. Furthermore, we know that RNA can catalyze nucleotide synthesis and act and as simple replicaters that could evolve first of all into more complicated protocells which could further evolve into more complicated single cellular and then multi-cellular life forms. Indeed, there is fossil evidence to show that something like this was going on.

Of course, we don’t at the present time understand all the details but there is nothing that rules out possibility of abiogenesis a priori. In fact, to reject it you are making an argument from ignorance. You, on the other hand cannot offer an alternative hypothesis that is scientifically testable. Can you? (smirk, smirk)

So what do you think of that Bradford?

(Zachriel, help me, help you.)

Comment by JOHN_A_DESIGNER — July 21, 2008 @ 11:14 pm

Thought Provoker Says:
July 22nd, 2008 at 12:06 am
Hi John,

On the off chance that you might actually want to try to make a convincing argument from the other side, try what I did. Figure out what basics you can defend and extrapolate with logic you believe.

Interconnected quantum effects that makes up a purposeful universe is something I can defend.

Surely, extraterrestrial contamination is something you could defend isn't it? (note the paper on the Murchison meteorite mentioned earlier in the thread).

Comment by Thought Provoker — July 22, 2008 @ 12:06 am

Bradford Says:
July 22nd, 2008 at 12:11 am
John A. Designer:

I think what Zachriel is trying to say here, Bradford, is that if we extrapolate the evolutionary process, which we already know is a completely natural process, backwards in time we find that there are simple organisms that evolve from simpler organism’s and we keep getting simpler and simpler and simpler till we reach a point where we have only organic compounds.

I know the other side believes in the sufficiency of natural forces even when those forces are unidentified but since they make such a point of being so sciency I must insist they live up to their self-appointed reputations for empirical rigor. Simpler to simpler. Simpler to more complex. Any direction it is looked upon presupposes the adaquacy of a self-replicating system, not a molecule. You don't assume the adaquacy of the ToR or QM. It is demonstrated or so we are continually lectured about. Fine. Make no exception so as to sneak naturalism in through the back door (Sorry Lewontin. Hope you don't have that copyrighted.)

Comment by Bradford — July 22, 2008 @ 12:11 am

Zachriel Says:
July 22nd, 2008 at 7:52 am
JOHN_A_DESIGNER: You can choose to help me if you wish. I will be honestly trying to represent your point of view.

I am impressed. That is precisely how one attempts to understand another's argument. Indeed, that is what we mean by hypothesis-testing. You tentatively make the assumption, then deduce specific and distinguishing empirical predictions entailed in the hypothesis.

JOHN_A_DESIGNER: I think what Zachriel is trying to say here, Bradford, is that if we extrapolate the evolutionary process, which we already know is a completely natural process, backwards in time we find that there are simple organisms that evolve from simpler organism’s and we keep getting simpler and simpler and simpler till we reach a point where we have only organic compounds.

That's correct. Though not definitive, it is sufficient to form a reasonable hypothesis.

JOHN_A_DESIGNER: Experiments like Stanley Millers abiogenesis experiment have demonstrated that given the right conditions certain organic molecules like amino acids can be formed rather easily.

We take the hypothesis and try to devise entailed predictions. In this case, that macromolecules might form under a variety of relevant conditions. More recent experiments have shown that purines are also synthesized, then concentrated through catalysis.

JOHN_A_DESIGNER: Furthermore, we know that RNA can catalyze nucleotide synthesis and act and as simple replicaters that could evolve first of all into more complicated protocells which could further evolve into more complicated single cellular and then multi-cellular life forms. Indeed, there is fossil evidence to show that something like this was going on.

The discovery of ribozymes removed one particular objection, the 'irreducible complexity' of the Central Dogma, that is, always nucleotide to enzyme.

JOHN_A_DESIGNER: Of course, we don’t at the present time understand all the details but there is nothing that rules out possibility of abiogenesis a priori.

This is also correct. This is not to say that objections are irrelevant. An objection may call into question the plausibility of one or another hypothesis.

JOHN_A_DESIGNER: In fact, to reject it you are making an argument from ignorance.

To reject abiogenesis without an argument is just obstinance.

To purport a scientific claim of a designer because of the lack of a valid theory of abiogenesis, while offering no scientific evidence of a designer (hypothesis-testing), is an argument from ignorance.

JOHN_A_DESIGNER: You, on the other hand cannot offer an alternative hypothesis that is scientifically testable. Can you? (smirk, smirk)

It's not always easy, but do I try to avoid the smirks.

Comment by Zachriel — July 22, 2008 @ 7:52 am

Zachriel Says:
July 22nd, 2008 at 7:56 am
Bradford: You don't assume the adaquacy of the ToR or QM. It is demonstrated or so we are continually lectured about.

The difference is that there are valid theories of Relativity and Quantum Mechanics. No one claims a complete theory of abiogenesis. However, abiogenesis is a testable hypothesis.

We often call a proposed explanation a theory, but all such theories of abiogenesis are incomplete and largely unverified.

Consider theories of the Moon's origin. Several theories vied for acceptance. Lack of empirical evidence left these theories in limbo for generations. Modern computer simulations provide convincing evidence that the Earth was struck by a planetoid early in its history, a theory which is supported by the unique geological characteristics of the Moon. But at no time did God A Designer Did It constitute a valid alternative scientific theory.

Comment by Zachriel — July 22, 2008 @ 7:56 am

chunkdz Says:
July 22nd, 2008 at 12:14 pm
Zachriel,

"Abiogenesis is a testable hypothesis."

How do you falsify it?

Comment by chunkdz — July 22, 2008 @ 12:14 pm

Zachriel Says:
July 22nd, 2008 at 1:20 pm
Zachriel: Abiogenesis is a testable hypothesis.

chunkdz: How do you falsify it?

I would revise my statement as Abiogenesis can encompass valid scientific hypotheses. The bare concept is too vague to constitute a valid hypothesis in and of itself.

How would you falsify the general claim that the moon was formed by natural (not artificial) processes? There is significant evidence concerning how masses have interacted and do interact, and various testable hypotheses concerning the natural formation of the Solar System, planets and Moon. To falsify the general claim would require convincing scientific evidence of artifice. Currently, there is no evidence of artifice in the origin of the Moon.

How would you falsify the general claim that the origin of life was due to natural (not artificial) processes? There is significant evidence concerning how life has evolved and does evolve, and various testable hypotheses concerning the origin of life. To falsify the general claim would require convincing scientific evidence of artifice. Currently, there is no evidence of artifice in the origin of life.

Comment by Zachriel — July 22, 2008 @ 1:20 pm

chunkdz Says:
July 22nd, 2008 at 2:56 pm
Z,

I would revise my statement as Abiogenesis can encompass valid scientific hypotheses. The bare concept is too vague to constitute a valid hypothesis in and of itself.

The same could be said for directed panspermia.

Currently, there is no evidence of artifice in the origin of life.

Sure there is. It's just that what others call rational design you call a lucky accident. Worldview colors perception.

Comment by chunkdz — July 22, 2008 @ 2:56 pm

Zachriel Says:
July 22nd, 2008 at 3:06 pm
Zachriel: The bare concept is too vague to constitute a valid hypothesis in and of itself.

chunkdz: The same could be said for directed panspermia.

Panspermia is speculative, and also lacks supporting evidence.

Zachriel: Currently, there is no evidence of artifice in the origin of life.

chunkdz: Sure there is.

Then state a clear hypothesis and the entailed, specific and distinguishing empirical predictions.

Comment by Zachriel — July 22, 2008 @ 3:06 pm

chunkdz Says:
July 22nd, 2008 at 4:14 pm
Panspermia is speculative, and also lacks supporting evidence.

Speculative - yes, devoid of support - no.

Then state a clear hypothesis and the entailed, specific and distinguishing empirical predictions.

Neither worldview is ready for this step yet. OOL is in the exploration stage.

Comment by chunkdz — July 22, 2008 @ 4:14 pm

Zachriel Says:
July 22nd, 2008 at 4:25 pm
chunkdz: Speculative - yes, devoid of support - no.

Please provide whatever scientific evidence you think supports panspermia.

chunkdz: Neither worldview is ready for this step yet.

Abiogenetics researchers propose and test hypotheses all the time.

Comment by Zachriel — July 22, 2008 @ 4:25 pm

chunkdz Says:
July 22nd, 2008 at 5:12 pm
Please provide whatever scientific evidence you think supports panspermia.

Bacteria that can survive the vacuum of space would lend a small amount of support to the idea, no?

Abiogenetics researchers propose and test hypotheses all the time.

That was a great article. It supports the idea of RNA being very fragile requiring controlled conditions, sophisticated equipment, and an intelligently designed program to incubate, amplify and isolate catalytic properties. Exactly what one would expect to find using a design paradigm. Of course, there is still much about the origin of life that is unknown.

Comment by chunkdz — July 22, 2008 @ 5:12 pm

Zachriel Says:
July 22nd, 2008 at 8:46 pm
chunkdz: Bacteria that can survive the vacuum of space would lend a small amount of support to the idea, no?

Without a clear statement of your claim, it's difficult to evaluate it. The volume of space is such that the likelihood of bacteria drifting from stellar system to stellar system is very low. Directed panspermia by dispersal is also exceedingly unlikely. However, it does make good science fiction.

chunkdz: Exactly what one would expect to find using a design paradigm.

The researchers were generating and testing hypotheses based on theories of natural abiogenesis. Is there a reason you are misrepresenting the research?

Comment by Zachriel — July 22, 2008 @ 8:46 pm

Kuma Says:
July 22nd, 2008 at 8:55 pm
Hey John,
After some thought, a place to start with thinking as honestly as possible about what a real world design theory might entail would have to be some kind of simulation theory. This seems highly possible and even useful to a human like intelligence designer of some type. There may be a problem to solve or an observation to make concerning the universe at large.

As we all know with more technological advances, simulations have become big business as entertainment and extremely useful to working out scientific problems. Along with that our understanding of AI increases daily which makes simulated human intelligence much closer to reality.

I think a line of questioning could begin under this premise. Of course this would have to come from QM or physics in general as opposed to biology, as the biology contained within the simulation would be part of the simulation… I'm trying to think of some kind of testable idea or line of questioning….

Perhaps starting with the question of the duality of particles and waves. Since scientist are still trying hard to answer the question of the needed observer (whether or not it is indeed needed). Perhaps the simulation is saving processing power by switching modes when not observed by an intelligent agent within the simulation.

Of course there is always the question of what type of observer can cause the wave function collapse? Has this been tested? can a cat or jellyfish cause the collapse? can an true AI cause the collapse(perhaps this will take some time)

Just throwing out what I would rationally have to allow as a real design theory. This removes all sky fairies and the questions of a meddlsome god as any scientist would have to agree it's better to let an experiment run it's course before throwing away or tampering with the test tube.

Of course this also tells us nothing about what the "real world" might be like but it does make our existence contingent on a "human like designer"

Just thought I'd throw that out…

Comment by Kuma — July 22, 2008 @ 8:55 pm

JOHN_A_DESIGNER Says:
July 22nd, 2008 at 11:13 pm
Zachriel, earlier you had this exchange with Chunkdz:

Zachriel: Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

chunkdz: Ho hum. Another appeal to luck.

Zachriel: It's not luck to say that a coin will land either heads or tails. Do you understand the Law of Small Numbers and how it applies to fixation?
There aren't enough small numbers to meet the many demands made of them. — Richard Guy

So, it’s about probability then, isn’t it? Many of the arguments against abiogenesis center around it’s low probability. Obviously the probability can’t be so low that it is a virtual impossibility. So then, what should we assume about the probability of the OoL? Does it have such a low probability that it’s little more than a lucky accident? Or, does it have a fairly high probability, so that given the right conditions life most likely will emerge?

Can we say anything about life elsewhere in the universe? What about the organic molecules that have been detected in interstellar space, or discovered in meteorites. If it is probable that life originated here on this planet can we use that evidence to extrapolate to other possible planets, especially since we are now beginning to detect new planets around other nearby stars?

Comment by JOHN_A_DESIGNER — July 22, 2008 @ 11:13 pm

Bradford Says:
July 22nd, 2008 at 11:47 pm
JOHN_A_DESIGNER:

So, it’s about probability then, isn’t it? Many of the arguments against abiogenesis center around it’s low probability. Obviously the probability can’t be so low that it is a virtual impossibility. So then, what should we assume about the probability of the OoL? Does it have such a low probability that it’s little more than a lucky accident? Or, does it have a fairly high probability, so that given the right conditions life most likely will emerge?

If probability or chance is at the root of abiogenesis then the door is open to a demonstration that abiogenesis is implausible based on chance or probability. If neither is the basis then what is the empirical evidence for causal determinism?

Comment by Bradford — July 22, 2008 @ 11:47 pm

nobody Says:
July 23rd, 2008 at 1:53 am
JAD says:

Obviously the probability can’t be so low that it is a virtual impossibility.

No. What's obvious is that you're wrong. The probability of the space shuttle (some of our best technology) assembling itself is zero and the probablility of life (even higher technology) poofing itself out of a chemical brew is also zero.

Comment by nobody — July 23, 2008 @ 1:53 am

Zachriel Says:
July 23rd, 2008 at 7:15 am
Zachriel: Racemization has not been shown to be an inherent barrier and may simply be due to fixation early in the process.

JOHN_A_DESIGNER: So, it’s about probability then, isn’t it?

The probability in question concerns well-known mathematics concerning fixation, so your comment is a non sequitur. Fixation occurs regardless of any theory of abiogenesis, heritable variation, or selection.

Neutral Drift and the Law of Small Numbers

Consider a population limited by circumstance to just two, with two variants in the population.

A, B

Let them reproduce.

A1, A2, B1, B2

Now, we keep two at random. These are the possibilities.

A1, A2
A1, B1
A1, B2
A2, B1
A2, B2
B1, B2

There is a one in three chance of forever losing one of the two variants. But let's assume that we end up with both variants. But then, over each succeeding generation, we are again faced with a one in three chance of forever losing one of the two variants. Sooner or later, we will have A, A or B, B. Fixation.

Now consider a population of three.

A, B, C

Let them reproduce.

A1, A2, B1, B2, C1, C2

Now choose three. There are twenty possibilities. Some of them include all three variants. But some don't. Even if all three variants make it into the next generation, we are again faced with a significant possibility of losing one of the variants forever. Eventually, we will lose one variant. Such as this.

A, A, B

Now reproduce again.

A1, A2, A3, A4, B1, B2

Again, choose three. Notice that there is a finite chance of keeping both variants. But there is also a finite chance of losing another variant forever. Eventually, this will happen. Fixation.

Which variant will become fixed? It's random. So in the first case, it is 1/2. In the second case, it is 1/3. But notice that it takes longer with the larger population. Indeed, Hardy-Weinberg proved that in an infinite (undisturbed) population, the rate of fixation is zero. But no population is infinite.

This is not an empirical result. It's arithmetic.

But to directly address your comment, no one can calculate the overall probability of abiogenesis without a valid theory. However, probability calculations are often used to test particular hypotheses.

JOHN_A_DESIGNER: Can we say anything about life elsewhere in the universe? What about the organic molecules that have been detected in interstellar space, or discovered in meteorites. If it is probable that life originated here on this planet can we use that evidence to extrapolate to other possible planets, especially since we are now beginning to detect new planets around other nearby stars?

Most researchers now believe the probability is very high that there is other life somewhere in the home galaxy. It is not yet possible to calculate an accurate probability, but knowledge about abiogenesis informs these questions.

Comment by Zachriel — July 23, 2008 @ 7:15 am

Zachriel Says:
July 23rd, 2008 at 7:18 am
nobody: the probablility of life (even higher technology) poofing itself out of a chemical brew is also zero.

That would appear to eliminate the *poof* hypothesis.

Comment by Zachriel — July 23, 2008 @ 7:18 am

Zachriel Says:
July 23rd, 2008 at 8:16 am
Zachriel: The probability in question concerns well-known mathematics concerning fixation, so your comment is a non sequitur. Fixation occurs regardless of any theory of abiogenesis, heritable variation (among offspring, i.e. mutation), or selection.

The reader would probably know what I meant from context, but I have edited the statement for clarity.

Comment by Zachriel — July 23, 2008 @ 8:16 am

chunkdz Says:
July 23rd, 2008 at 11:36 am
Zachriel,

Without a clear statement of your claim, it's difficult to evaluate it. The volume of space is such that the likelihood of bacteria drifting from stellar system to stellar system is very low. Directed panspermia by dispersal is also exceedingly unlikely.

Science does not stop investigating just because things look "unlikely" at first glance, or because some guy on a blog feels skeptical. Bacteria that seem adapted for survival in the vacuum of space is one piece of evidence that makes scientists keep investigating.

So much for your claim that there is no supporting evidence.

The researchers were generating and testing hypotheses based on theories of natural abiogenesis. Is there a reason you are misrepresenting the research?

Nope. I fully realize that this is an important first step for the natural paradigm - proving that this type of catalysis *can* happen, albeit under very tight controls and conditional restraints.

But I also see that this supports the idea of RNA as exceedingly fragile, requiring sophisticated apparatus and a very controlled environment in which to do it's thing. Intelligent design was required to make this happen.

Now, if the researchers had discovered some kind of extracellular RNA catalyzing away in a lipid membrane on a clay substrate in the backcountry of New Zealand, I might say this FULLY and EXCLUSIVELY supports the natural paradigm. As it stands though, the data seems to lend support to both paradigms.

Is that ok with you? Can evidence be viewed from more than one angle, or should there be an academic standard that says all data must be viewed only the way the researchers viewed it?

Comment by chunkdz — July 23, 2008 @ 11:36 am

chunkdz Says:
July 23rd, 2008 at 12:03 pm
OT, but made me lol!

Zachriel, bragging about his own humility: "It's not always easy, but do I try to avoid the smirks."

Zachriel, 4 minutes later: "But at no time did ~~God~~ A Designer Did It constitute a valid alternative scientific theory."

In the smirky words of John A. Davison, "I love it so!"

Comment by chunkdz — July 23, 2008 @ 12:03 pm

Zachriel Says:
July 23rd, 2008 at 1:12 pm
chunkdz: Bacteria that seem adapted for survival in the vacuum of space is one piece of evidence that makes scientists keep investigating.

Just because the ancient Egyptian sailors plied the Mediterranean in ships that might have survived being blown across the Atlantic to the Americas, is not evidence that they were or that they affected the native cultures there. One could use this speculation to devise a testable hypothesis, though.

chunkdz: Science does not stop investigating just because things look "unlikely" at first glance, or because some guy on a blog feels skeptical.

You didn't answer the objection. Nor did you clarify your claim. However, you are more than welcome to investigate whatever it is you're claiming with whatever means you choose. Let us know if you find any scientific evidence to support whatever it is you're claiming.

Zachriel: The researchers were generating and testing hypotheses based on theories of natural abiogenesis. Is there a reason you are misrepresenting the research?

chunkdz: … But I also see that this supports the idea of RNA as exceedingly fragile, requiring sophisticated apparatus and a very controlled environment in which to do it's thing.

It takes sophisticated apparatus built in very controlled environments to create artificial satellites. That doesn't mean all satellites are artificial.

The fragility of RNA is an issue for abiogenesis, but there are a number of plausible solutions, such as segregation, but also precursor nucleic acids, such as PNA.

chunkdz: Intelligent design was required to make this happen.

That's a claim, but you haven't provided any scientific evidence to support it.

You still don't seem to understand the scientific method. It means proposing a hypothesis, deducing its entailed implications, then testing for specific and distinguishing empirical predictions. That some bacteria are hardy enough to survive interstellar space might allow reasonable speculation. But because bacteria are hardy for other, mundane reasons, it doesn't distinguish the cases.

Zachriel, 4 minutes later: But at no time did God A Designer Did It constitute a valid alternative scientific theory.

That's not a smirk, but sarcasm.

Comment by Zachriel — July 23, 2008 @ 1:12 pm

chunkdz Says:
July 23rd, 2008 at 1:57 pm
Zachriel,

Just because the ancient Egyptian sailors plied the Mediterranean in ships that might have survived being blown across the Atlantic to the Americas, is not evidence that they were or that they affected the native cultures there.

Actually, it is. Not conclusive evidence, perhaps not even mildly compelling evidence, but it certainly is evidence that lends support to the idea.

You didn't answer the objection. Nor did you clarify your claim. However, you are more than welcome to investigate whatever it is you're claiming with whatever means you choose. Let us know if you find any scientific evidence to support whatever it is you're claiming.

If life on earth was seeded from outside of our planet, then bacteria adapted for life in space is supporting evidence for this idea. Not very strong evidence, but evidence all the same.

It takes sophisticated apparatus built in very controlled environments to create artificial satellites. That doesn't mean all satellites are artificial.

That's true. Dish Network could have simply formed from cosmic dust.

The fragility of RNA is an issue for abiogenesis, but there are number of plausible solutions, such as segregation, but also precursor nucleic acids, such as PNA.

Yup. But those are speculations. However, we have direct evidence that these techniques can work in the lab when administered by intelligent designers.

chunkdz: Intelligent design was required to make this happen.

Zachriel: That's a claim, but you haven't provided any scientific evidence to support it.

Are you saying the scientists weren't intelligent?

That some bacteria are hardy enough to survive interstellar space might allow reasonable speculation.

So you now admit that it is evidence that lends support to panspermia.

But because bacteria are hardy for other, mundane reasons, it doesn't distinguish the cases.

That's true. Certainly no smoking gun. But it's slightly more compelling than if bacteria *couldn't* survive in outer space. After all, there really are relatively few smoking guns in science. It's more about a slow, gradual accumulation of evidence.

Evidence. Just enough for reasonable speculation, as you said.

I couldn't help but notice that you neglected my question. It really is a central one for me, so if you wouldn't mind,

"Is that ok with you? Can evidence be viewed from more than one angle, or should there be an academic standard that says all data must be viewed only the way the researchers viewed it?"

Comment by chunkdz — July 23, 2008 @ 1:57 pm

Zachriel Says:
July 23rd, 2008 at 2:25 pm
Zachriel: Just because the ancient Egyptian sailors plied the Mediterranean in ships that might have survived being blown across the Atlantic to the Americas, is not evidence that they were or that they affected the native cultures there.

chunkdz: Actually, it is. Not conclusive evidence, perhaps not even mildly compelling evidence, but it certainly is evidence that lends support to the idea.

You never clarified your claim. Is this because you find it easier to avoid having to support your claim? You also never answered the objection I raised above. Is this because you really don't care whether your claims can be supported or not?

It's possible that aliens traveled to the Earth right after it cooled enough for life to exist, then planted little organic nanobots, and a monolith on Europa. Or ethereal spirits add elan vital (undetectable except to the initiati) to the water supply. Or the world was created Last Thursday. I can speculate too.

chunkdz: If life on earth was seeded from outside of our planet, then bacteria adapted for life in space is supporting evidence for this idea.

If you can show that bacteria are adapted for interstellar travel (rather than having characteristics that evolved due to terrestrial conditions that might happen to allow survival during long interstellar voyages), then that might be evidence.

Zachriel: It takes sophisticated apparatus built in very controlled environments to create artificial satellites. That doesn't mean all satellites are artificial.

chunkdz: That's true. Dish Network could have simply formed from cosmic dust.

Earth is a satellite that was formed from cosmic dust. Or maybe someone seeded its original formation with a single pebble. There's no evidence of this, but it could have happened that way.

Zachriel: That some bacteria are hardy enough to survive interstellar space might allow reasonable speculation.

chunkdz: So you now admit that it is evidence that lends support to panspermia.

Speculation is not evidence. You still have to form a hypothesis and test it.